Structure of PDB 6ncj Chain A Binding Site BS01

Receptor Information

>6ncj Chain A (length=142) Species: 11676 (Human immunodeficiency virus 1)

SSPGIWQLDCTHLEGKVILVAVHVASGYIEAEVIPAETGQETAYFLLKLA
GRWPVKTVHTDNGSNFTSTTVKAACWWAGIKQEDGIVIESMNKELKKIIG
QVRDQAEHLKTAVQMAVFIHNHKRKGGYSAGERIVDIIATDI

Ligand information

• Ligand ID: KJJ
• InChI: InChI=1S/C35H41FN2O4/c1-20-24-12-9-15-41-32(24)28(36)17-25(20)31-27-19-38(18-23-16-26(23)22-10-7-6-8-11-22)14-13-29(27)37-21(2)30(31)33(34(39)40)42-35(3,4)5/h6-8,10-11,17,23,26,33H,9,12-16,18-19H2,1-5H3,(H,39,40)/t23-,26+,33+/m1/s1
• InChIKey: BXDYSLFANINKPQ-VEWAMZQOSA-N
• SMILES:
  CACTVS 3.385: Cc1nc2CCN(C[C@H]3C[C@H]3c4ccccc4)Cc2c(c5cc(F)c6OCCCc6c5C)c1[C@H](OC(C)(C)C)C(O)=O
  OpenEye OEToolkits 2.0.7: Cc1c(cc(c2c1CCCO2)F)c3c4c(nc(c3[C@@H](C(=O)O)OC(C)(C)C)C)CCN(C4)C[C@H]5C[C@H]5c6ccccc6
  CACTVS 3.385: Cc1nc2CCN(C[CH]3C[CH]3c4ccccc4)Cc2c(c5cc(F)c6OCCCc6c5C)c1[CH](OC(C)(C)C)C(O)=O
  OpenEye OEToolkits 2.0.7: Cc1c(cc(c2c1CCCO2)F)c3c4c(nc(c3C(C(=O)O)OC(C)(C)C)C)CCN(C4)CC5CC5c6ccccc6
• Formula: C35 H41 F N2 O4
• PDB chain: 6ncj Chain A Residue 305

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6ncj 5,6,7,8-Tetrahydro-1,6-naphthyridine Derivatives as Potent HIV-1-Integrase-Allosteric-Site Inhibitors.
• Resolution: 2.0 Å
• Binding residue (original residue number in PDB): Q95 T124 T125 A128 A129 W132
• Binding residue (residue number reindexed from 1): Q40 T69 T70 A73 A74 W77
• Annotation score: 1
• Binding affinity: MOAD: ic50=0.024uM
  PDBbind-CN: -logKd/Ki=7.62,IC50=0.024uM

Gene Ontology

Molecular Function

• GO:0003676 nucleic acid binding

Biological Process

• GO:0015074 DNA integration

External links

• PDB: RCSB:6ncj, PDBe:6ncj, PDBj:6ncj
• PDBsum: 6ncj
• PubMed: 30609350
• UniProt: F2WR52